Epigenetic regulation of development and pathogenesis in fungal plant pathogens

Evidently, epigenetics is at forefront in explaining the mechanisms underlying the success of human pathogens and in the identification of pathogen‐induced modifications within host plants. However, there is a lack of studies highlighting the role of epigenetics in the modulation of the growth and pathogenicity of fungal plant pathogens. In this review, we attempt to highlight and discuss the role of epigenetics in the regulation of the growth and pathogenicity of fungal phytopathogens using Magnaporthe oryzae, a devastating fungal plant pathogen, as a model system. With the perspective of wide application in the understanding of the development, pathogenesis and control of other fungal pathogens, we attempt to provide a synthesized view of the epigenetic studies conducted on M. oryzae to date. First, we discuss the mechanisms of epigenetic modifications in M. oryzae and their impact on fungal development and pathogenicity. Second, we highlight the unexplored epigenetic mechanisms and areas of research that should be considered in the near future to construct a holistic view of epigenetic functioning in M. oryzae and other fungal plant pathogens. Importantly, the development of a complete understanding of the modulation of epigenetic regulation in fungal pathogens can help in the identification of target points to combat fungal pathogenesis.     

Linkage between bacterial and fungal rhizosphere communities in hydrocarbon-contaminated soils is related to plant phylogeny

Phytoremediation is an attractive alternative to excavating and chemically treating contaminated soils. Certain plants can directly bioremediate by sequestering and/or transforming pollutants, but plants may also enhance bioremediation by promoting contaminant-degrading microorganisms in soils. In this study, we used high-throughput sequencing of bacterial 16S rRNA genes and the fungal internal transcribed spacer (ITS) region to compare the community composition of 66 soil samples from the rhizosphere of planted willows (Salix spp.) and six unplanted control samples at the site of a former petrochemical plant. The Bray–Curtis distance between bacterial communities across willow cultivars was significantly correlated with the distance between fungal communities in uncontaminated and moderately contaminated soils but not in highly contaminated (HC) soils (>2000 mg kg⁻¹ hydrocarbons). The mean dissimilarity between fungal, but not bacterial, communities from the rhizosphere of different cultivars increased substantially in the HC blocks. This divergence was partly related to high fungal sensitivity to hydrocarbon contaminants, as demonstrated by reduced Shannon diversity, but also to a stronger influence of willows on fungal communities. Abundance of the fungal class Pezizomycetes in HC soils was directly related to willow phylogeny, with Pezizomycetes dominating the rhizosphere of a monophyletic cluster of cultivars, while remaining in low relative abundance in other soils. This has implications for plant selection in phytoremediation, as fungal associations may affect the health of introduced plants and the success of co-inoculated microbial strains. An integrated understanding of the relationships between fungi, bacteria and plants will enable the design of treatments that specifically promote effective bioremediating communities.     

Molecular characterization of Legionella populations present within slow sand filters used for fungal plant pathogen suppression in horticultural crops

The total bacterial community of an experimental slow sand filter (SSF) was analyzed by denaturing gradient gel electrophoresis (DGGE) of partial 16S rRNA gene PCR products. One dominant band had sequence homology to Legionella species, indicating that these bacteria were a large component of the SSF bacterial community. Populations within experimental and commercial SSF units were studied by using Legionella-specific PCR primers, and products were studied by DGGE and quantitative PCR analyses. In the experimental SSF unit, the DGGE profiles for sand column, reservoir, storage tank, and headwater tank samples each contained at least one intense band, indicating that a single Legionella strain was predominant in each sample. Greater numbers of DGGE bands of equal intensity were detected in the outflow water sample. Sequence analysis of these PCR products showed that several Legionella species were present and that the organisms exhibited similarity to strains isolated from environmental and clinical samples. Quantitative PCR analysis of the SSF samples showed that from the headwater sample through the sand column, the number of Legionella cells decreased, resulting in a lower number of cells in the outflow water. In the commercial SSF, legionellae were also detected in the sand column samples. Storing prefilter water or locating SSF units within greenhouses, which are often maintained at temperatures that are higher than the ambient temperature, increases the risk of growth of Legionella and should be avoided. Care should also be taken when used filter sand is handled or replaced, and regular monitoring of outflow water would be useful, especially if the water is used for misting or overhead irrigation.     

The microbiology of soils under successive wheat crops in relation to take-all disease

Abstract Thirty-eight wheat fields in southern England were sampled in an attempt to correlate the amount of take-all disease with 35 microbiological and chemical measurements of soil. There was little correlation between field take-all and pot tests to determine soil infectivity. Myxogastrids were important components of the soil population, being up to half of the amoebal population, and most soils contained dictyostelids, reticulate amoebae and myxobacteria. Amoebae, ciliates, bacteria and saprophytic fungi were recorded for all soils. pH was a major determinant of soil populations, being clearly correlated with fungal abundance and with numbers of ciliates, dictyostelids and bacteria. Principal component analysis separated dictyostelids from the other soil amoebae and again showed the importance of pH in determining soil microbial populations. Take-all was negatively correlated with soil fertility and positively related to nematodes and myxobacteria, but this was probably an effect of take-all, and represented saprophytic growth on dead roots rather than being a cause. Reticulate amoebae and dictyostelids were both correlated with low levels of take-all. This study emphasises the large number of interrelated populations of soil microorganisms which could have an effect on the severity of take-all infections.     

Turnover of organic nitrogen in soils and its availability to crops

The root development of barley seedlings grown for one week in an aerated nutrient solution was studied in the presence of dissolved organic matter from an aqueous chestnut leaf litter extract. In particular, the different effects of low and high molecular weight fractions (small molecules: molecular weight <1000; large molecules: >10,000) of the leaf litter extract were examined. In the presence of large molecules root growth was inhibited, an irregular root tip morphology was observed, and Ca and Mg concentrations in the shoots were lower than in control plants. These phytotoxic effects were not caused by the formation of an impermeable layer of large molecules on the root surfaces that lower accessibility for nutrient cations as inferred from voltammetric experiments. A germination assay using spruce seeds, however, indicated allelochemical effects of large molecules, which exhibit a higher aromaticity than the small molecules as indicated by spectroscopic characterisation. In the growth experiments with small molecules, no influence on the root development of barley was evident, but an increase of Ca and Mg in the shoots was detected. During these growth experiments, a large amount of the small molecules, mainly simple phenols and amino acids, disappeared from the nutrient solution. The loss of small molecules was most likely the effect of mineralisation.Abbreviations DOC dissolved organic carbon - DOM dissolved organic matter - LLE leaf litter extract - MW molecular weight - HMDE hanging mercury drop electrode     

Dynamics of organic matter in soils

Summary Dynamics of C, N, S, and to some extent P are expressed by a knowledge of the size and turnover rates of plant constituents such as soluble C and N components, cellulose and hemicellulose, and lignin. Soil organic matter constituents include: the microbial biomass as determined chemically or microscopically, non-biomass active components determined by isotopic dilution, stabilized N constituents for which good techniques are not yet available, and resistant or old C and associated N determined by carbon dating. The processes involved in the nutrient transformations and transfers are reasonably well understood. The control mechanisms require further elucidation to be able to extrapolate from the laboratory to the field, and between field sites. Major control mechanisms requiring further insight include the effects of C availability on transformations of C and N. The other control for which every little is known is that of spatial compartmentalization. Compartmentalization ranges from landscape or management sequences to pedogenic layers, rhizosphere-mycorrhizal effects, clay-sesquioxide surfaces, aggregation, localized enzymes, and microbial effects such as membrane boundaries. Control mechanisms for concurrent mineralization-immobilization, the stabilization of microbial products, and the relative role of the biomass as a catalyst rather than as a source-sink for nutrients, must be understood. There is potential for combining a knowledge of microbial production and turnover with that of the roles of the soil organic active fraction as a temporary storehouse for nutrients. This, in conjunction with management techniques such as zero tillage and crop rotation, should make it possible to better utilize soil and fertilizer N, especially in areas of the world where the cost of nutrients is high relative to the value of the crop grown.Introductory lecture     

Water-soluble organic matter in forest soils

By applying a modified gel permeation technique, the molecular-size distribution (MSD) and complexing properties of water-soluble organic matter (WSOM), isolated from the A_h horizon under stands with either Douglas-fir, European beech or Scots pine were established. Both with respect to MSD and complexing properties, the dissolved organic matter was highly similar. WSOM was comprised of compounds apparently high in molecular weight (>1 kDa) and with a complexing capacity of 1.0±0.1 mol mg^–1 carbon as determined for Cu(II) at pH 5.5 and 0.01 M ionic strength. The effect of WSOM on the partitioning of cations between soil solid phase and soil solution was evaluated in several soil batch experiments using loamy sand or sandy soil material. Although a large part of WSOM was sorbed to the soil matrix, Al, Cu, Fe and Pb were solubilized in considerable amounts by complexation. The Mn concentration in the soil solution was also significantly increased but this probably resulted from a redox reaction, with certain constituents of WSOM serving as electron donor. With a decrease in soil pH, cation mobilization by WSOM was significantly lower as a result of increased sorption and a decrease in complexing capacity of the soluble organics. Application of several low MW aliphatic and phenolic acids gave results similar to the results obtained with WSOM.     

Influence of soil fauna on fungal plant pathogens in agricultural and horticultural systems

An understanding of the ecology of plant pathogens is crucial for the development of agricultural and horticultural growing systems that enhance plant health. One important group of organisms that influences plant pathogen survival and dispersal is the soil fauna. This review deals with known and possible interactions between soil animals and different groups of fungal plant pathogens. It is suggested that facultative saprophytes may be affected considerably by mycelial grazing by soil animals, while obligate pathogens may be more influenced by animals that ingest spores and other types of propagules. Both types of pathogens can also be influenced by indirect interactions with the soil fauna. Manipulating the soil environment for enhancement of beneficial soil animals that consume pathogens seems to be a realistic possibility for sustainable agriculture and horticulture.     

The retention of organic matter in soils

The turnover of C in soils is controlled mainly by water regimes and temperature, but is modified by factors such as size and physicochemical properties of C additions in litter or root systems, distribution of C throughout the soil as root systems, or addition as litter, distribution of C within the soil matrix and its interaction with clay surfaces.Soil factors which retard mineralization of C in soils are identified from correlations of C contents of soils with other properties such as clay content and base status. The rate and extent of C mineralization depends on the chemistry of the added organic matter and interaction with clays of the microbial biomass and metabolites.The organomineral interactions are shown to depend on cation bridges involving mainly Ca in neutral to alkaline soils, Al in acid soils and adsorption of organic materials on iron oxide surfaces. The various organomineral interactions lead to aggregations of clay particles and organic materials, which stabilizes both soil structure and the carbon compounds within the aggregates.     

Biological potential of fungal inocula for bioaugmentation of contaminated soils

The suitability of the fluorescein diacetate hydrolyzing activity (FDA) assay for determining the biological potential (ie fungal biomass produced per unit of substrate) of solid pelleted fungal inoculum intended for use in the bioaugmentation of contaminated soils with white-rot fungi, was evaluated. FDA activity of the white-rot fungusPhanerochaete chrysosporium grown on pelleted substrates and on agar was found to be proportional to quantities of fungal ergesterol and fungal dry matter, respectively. Inoculum biological potential was found to be greatly influenced by substrate formulation and structure, and temperature. Biological potential and the type of carrier influenced the ability ofP. chrysosporium to tolerate pentachlorophenol (PCP).Phanerochaete chrysosporium andTrametes versicolor introduced into PCP-contaminated soil on pellets with higher biological potential and higher nitrogen content (C:N ratio of 501), did not remove PCP more efficiently than when the fungi were introduced on pellets with a lower biological potential (C:N ratio of 3091). However, under the latter conditions most of the PCP was transformed to pentachloroanisole (PCA). In soil inoculated withT. versicolor on pellets with high biological potential, higher manganese peroxidase activity was detected compared to soil inoculated with pellets with a lower biological potential.     

Soil organic matter and yield of forest and tree crops

Summary Three hundred and sixty eight soil samples collected from the surface layers of plantations of coffee (Coffea robusta) andGmelina arborea (a forest tree crop) were analyzed for organic carbon, total nitrogen and loss-on-ignition as the case might be. The aim was to investigate the direct influence of soil organic matter on the yield of tree crops in different ecological zones of Nigeria. Coffee yield collected at different harvests and total coffee yield were seperately regressed on soil organic carbon content. In most cases, positive regressions of coffee yield on soil organic carbon were recorded. Consistent positive correlations between each of indicators of soil organic matter and girth ofGmelina arborea were recorded in the order of organic carbon, nitrogen and loss-on-ignition. The relationship between C: N ratio and the performance of Gmelina depended on which of organic carbon and soil nitrogen was more influential at a particular location.     

园艺作物成熟和衰老的分子生物学

对园艺作物乙烯和果实成熟、乙烯生物合成途径中二个关键酶ACC合成酶和ACC氧化酶的分子特性,基因克隆和表达及转基因研究等方面问题进行了评述。     

膜对采后园艺作物衰老的影响

植物衰老是由内在和外部环境因素所诱导和引起的一种主动过程 ,其中膜的劣变是这种过程早期的表现形式和基本特征。简要评述了膜系统对采后园艺作物的衰老作用。有证据表明膜系统破坏是采后园艺作物衰老的关键事件。膜脂生物化学和生物物理性质的变化、酶促和非酶促的过氧化作用导致了膜特性的改变和功能上的失调 (如离子泄漏和细胞去区域化 )。这样 ,反过来又进一步引起细胞代谢异常 ,并加速衰老进程。目前 ,膜系统对采后园艺作物衰老的作用过程正逐步得到阐明     

Soil fungal and bacterial responses to conversion of open land to short‐rotation woody biomass crops

Short‐rotation woody biomass crops (SRWCs) have been proposed as an alternative feedstock for biofuel production in the northeastern US that leads to the conversion of current open land to woody plantations, potentially altering the soil microbial community structures and hence functions. We used pyrosequencing of 16S and 28S rRNA genes in soil to assess bacterial and fungal populations when ‘marginal’ grasslands were converted into willow (Salix spp.) and hybrid poplar (Populus spp.) plantations at two sites with similar soils and climate history in northern Michigan (Escanaba; ES) and Wisconsin (Rhinelander; RH). In only three growing seasons, the conversion significantly altered both the bacterial and fungal communities, which were most influenced by site and then vegetation. The fungal community showed greater change than the bacterial community in response to land conversion at both sites with substantial enrichment of putative pathogenic, ectomycorrhizal, and endophytic fungi associated with poplar and willow. Conversely, the bacterial community structures shifted, but to a lesser degree, with the new communities dissimilar at the two sites and most correlated with soil nutrient status. The bacterial phylum Nitrospirae increased after conversion and was negatively correlated to total soil nitrogen, but positively correlated to soil nitrate, and may be responsible for nitrate accumulation and the increased N₂O emissions previously reported following conversion at these sites. The legacy effect of a much longer grassland history and a second dry summer at the ES site may have influenced the grassland (control) microbial community to remain stable while it varied at the RH site.     

Interactions between functionally diverse fungal mutualists inconsistently affect plant performance and competition

Plants form mutualistic relationship with a variety of belowground fungal species. Such a mutualistic relationship can enhance plant growth and resistance to pathogens. Yet, we know little about how interactions between functionally diverse groups of fungal mutualists affect plant performance and competition. We experimentally determined the effects of interaction between two functional groups of belowground fungi that form mutualistic relationship with plants, arbuscular mycorrhizal (AM) fungi and Trichoderma, on interspecific competition between pairs of closely related plant species from four different genera. We hypothesized that the combination of two functionally diverse belowground fungal species would allow plants and fungi to partition their symbiotic relationships and relax plant–plant competition. Our results show that: 1) the AM fungal species consistently outcompeted the Trichoderma species independent of plant combinations; 2) the fungal species generally had limited effects on competitive interactions between plants; 3) however, the combination of fungal species relaxed interspecific competition in one of the four instances of plant–plant competition, despite the general competitive superiority of AM fungi over Trichoderma. We highlight that the competitive outcome between functionally diverse fungal species may show high consistency across a broad range of host plants and their combinations. However, despite this consistent competitive hierarchy, the consequences of their interaction for plant performance and competition can strongly vary among plant communities.     

Decomposition of organic matter by fungi in saline soils

The object of the present investigation was to study the fungal decomposition of organic matter from different sources, added to the saline soils. The organic matter added was in the form of fresh cuttings of two salt tolerant harbaceous plants namelyDiplachne fusca (Kallar grass) andSesbania aculeata (Dhancha). In addition to these treatments, farm yard manure and press mud (waste of sugar industry) were also used as a source of organic matter. Twelve combinations of these treatments were studied. A number of fungi were isolated from differently treated saline soils incubated at 30 °C. Among the fungi isolatedAspergillus spp. andFusarium solani had the highest frequency of occurrence. The relative cellulolytic ability of 10 fungal species was also estimated.Alternaria humicola andNigrospora sp. were found to be the most cellulolytic among the fungi isolated. The decrease in organic matter due to microbial decomposition was found to be most rapid during first two weeks of incubation. Among the treatments with one organic matter source, press mud produced maximum humus equal to 0.28 %. The pH and electrical conductivity increased slightly due to the closed system where no leaching took place.     

Sink development and dry matter distribution in storage root crops

Events during early development are examined for their contribution to dry matter distribution in the mature plant. It is concluded that timing of initiation of the storage root is not a major cause of differences between cultivars of carrot. These may airse from differences in the control of partitioning of assimilate at storage organ initiation. Root crop species may be affected differently by environmental factors such as density as a result of different thresholds of response of sink development to source stimuli.